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Crystal structure of human CDK8/CYCC in complex with compound 4 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[2-(morpholin-4-yl)ethyl]urea)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RGF PDB ENTRY 3RGF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293.15 20% PEG3350, 0.2 M sodium formate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.487 α = 90 b = 71.847 β = 90 c = 171.042 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 85.52 99.9 0.114 6.2 8 18292 18292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.24 99.7 0.511 1.5 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3RGF 3 85.52 18292 17610 630 99.95 0.20381 0.20381 0.20256 0.23852 0.2364 RANDOM 49.997
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.98 -0.1 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.903 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.011 r_scbond_it 1.91 r_mcangle_it 1.456 r_mcbond_it 1.262 r_angle_refined_deg 1.088 r_angle_other_deg 0.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.903 r_dihedral_angle_4_deg 12.76 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.011 r_scbond_it 1.91 r_mcangle_it 1.456 r_mcbond_it 1.262 r_angle_refined_deg 1.088 r_angle_other_deg 0.892 r_nbd_refined 0.162 r_nbtor_refined 0.16 r_symmetry_vdw_other 0.145 r_mcbond_other 0.144 r_symmetry_vdw_refined 0.136 r_nbd_other 0.125 r_xyhbond_nbd_refined 0.1 r_symmetry_hbond_refined 0.093 r_nbtor_other 0.074 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4919 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 32
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling